Re: Bio::AlignIO help needed...

[Athanasius]

Hello HelplessEskimo, and welcome to the Monastery!

Although it looks bizarre, that is simply the error message thrown by Bio::AlignIO->new() when the specified file does not exist. I verified this as follows:

 1:50 >perl -MBio::AlignIO -wE "my $out = Bio::AlignIO->new(-file => '
+X.fasta', -format => 'fasta');"

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file 'X.fasta': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw C:/Perl/Strawberry/strawberry-perl-5.20.
+0.1-64bit-PDL/perl/site/lib/Bio/Root/Root.pm:449
STACK: Bio::Root::IO::_initialize_io C:/Perl/Strawberry/strawberry-per
+l-5.20.0.1-64bit-PDL/perl/site/lib/Bio/Root/IO.pm:270
STACK: Bio::AlignIO::_initialize C:/Perl/Strawberry/strawberry-perl-5.
+20.0.1-64bit-PDL/perl/site/lib/Bio/AlignIO.pm:401
STACK: Bio::AlignIO::new C:/Perl/Strawberry/strawberry-perl-5.20.0.1-6
+4bit-PDL/perl/site/lib/Bio/AlignIO.pm:311
STACK: Bio::AlignIO::new C:/Perl/Strawberry/strawberry-perl-5.20.0.1-6
+4bit-PDL/perl/site/lib/Bio/AlignIO.pm:332
STACK: -e:1
-----------------------------------------------------------

 1:51 >

(There is no such file in my current directory.)

So, I suggest you add the following immediately before the call to Bio::AlignIO->new():

use Cwd;
printf "Current working directory: '%s'\n", getcwd;
printf "Fasta file to read:        '%s'\n", $array[3];

to verify that the -file parameter you are passing to new really does name a file which exists in the current working directory.

Hope that helps,